GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ald-dh-CoA in Lactobacillus delbrueckii ZN7a-9

Align acetaldehyde dehydrogenase (acetylating) (EC 1.2.1.10) (characterized)
to candidate WP_002876377.1 B506_RS00085 aldehyde dehydrogenase family protein

Query= BRENDA::B0K315
         (466 letters)



>NCBI__GCF_000387565.1:WP_002876377.1
          Length = 464

 Score =  194 bits (494), Expect = 4e-54
 Identities = 125/406 (30%), Positives = 208/406 (51%), Gaps = 16/406 (3%)

Query: 36  IFNDVNEAVECAKEAQKKFALMDLEKREEIIAAIREACVNNARLLAEIACSETGRGRVED 95
           I+++++  V  + EA  +      E  +++   I +   +NAR LA++A  ETGRG+VED
Sbjct: 19  IYHNIDILVNKSHEALAQMDDFSQEDVDKLCQVIEKVGEDNARYLAQMAVDETGRGKVED 78

Query: 96  KVAKNILAAKKTPGTEDLKPTAWTG----DRGLTLVEMA-PVGVIASITPVTNPTATIIN 150
           KV KN  AA+     E +K     G    D+   L+++A P+GVIA +TPVTNPT+T+I 
Sbjct: 79  KVTKNTYAAQTI--WESMKDMKTVGVIEEDKQEGLMKIAEPIGVIAGVTPVTNPTSTVIF 136

Query: 151 NTISMLAAGNAVVFNPHPSAKKTSNKAVEIINEAILKVGAPNGLVCSINNPTIQTAQKLM 210
             +  + + N ++F  HP A+K   +  ++I EA +  GAP   +  I +P++     LM
Sbjct: 137 KAMIAMKSKNTIIFGFHPQAQKCCVETAKLIKEATVAAGAPENWIQWIEHPSLTATTALM 196

Query: 211 EHPEVNMVVVTGGKAVVQTALRCGKKVIGAGAGNPPVVVDETADIVKAAHDIACGASFDN 270
            +P+V +V+ TGG  +V+ A   GK  +G G GN P  +++TADI ++ +DI    +FDN
Sbjct: 197 NNPKVQIVLATGGPGMVKAAYSTGKPALGVGPGNGPSYIEKTADIEQSVNDIVLSKTFDN 256

Query: 271 NLPCIAEKEIIAVERIADTLLERMKREGAYVLHGKDIDRMTELIF--QGGAINKDLIGRD 328
            + C +E  ++  + + D + E   +   Y L   +I    E     + G +   + G+ 
Sbjct: 257 GMICASENSVVVDKEVYDQVKEAFLKRHCYFLKADEIKLFEEHFIDPRRGTVAGPMAGKS 316

Query: 329 AHFILSQIGIETGKDIRLVVMP---VDVSHPLVYHEQLMPVIPFVTVPTVEEAINLAVKA 385
           A  I    G+    D +++V     V   +PL   E+L PV          +A  +    
Sbjct: 317 AVKIAEMCGVTVPADTQVIVAEYSGVGPKYPL-SAEKLSPVFTLYKAENSAQAFKICTDL 375

Query: 386 --EGGNRHTAMMHSKNVENMTAFARAIQTTIFVKNAPSYAGIGFGG 429
              GG  HTA +H++N + +  FA A+     + N+P+  G G GG
Sbjct: 376 LNYGGRGHTAGIHTQNSKVIRKFAFAMSACRILVNSPAALG-GIGG 420


Lambda     K      H
   0.317    0.133    0.377 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 489
Number of extensions: 28
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 466
Length of database: 464
Length adjustment: 33
Effective length of query: 433
Effective length of database: 431
Effective search space:   186623
Effective search space used:   186623
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory